CompaRNA - on-line benchmarks of RNA structure prediction methods

CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Table of contents:

Overview

Performance Plots

Performance of MXScarna(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of RNASLOpt - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for MXScarna(20) & RNASLOpt [.zip] - may take several seconds...

Overview

Metric	MXScarna(20)		RNASLOpt
MCC	0.501	>	0.467
Average MCC ± 95% Confidence Intervals	0.462 ± 0.279	<	0.514 ± 0.309
Sensitivity	0.401	>	0.383
Positive Predictive Value	0.632	>	0.577
Total TP	67	>	64
Total TN	25787	>	25782
Total FP	58	>	53
Total FP CONTRA	4	<	11
Total FP INCONS	35	<	36
Total FP COMP	19	>	6
Total FN	100	<	103
P-value	0.0

Performance plots

Performance of MXScarna(20) - scored higher in this pairwise comparison

1. Total counts & total scores for MXScarna(20)

Total Base Pair Counts
Total TP	67
Total TN	25787
Total FP	58
Total FP CONTRA	4
Total FP INCONS	35
Total FP COMP	19
Total FN	100

Total Scores
MCC	0.501
Average MCC ± 95% Confidence Intervals	0.462 ± 0.279
Sensitivity	0.401
Positive Predictive Value	0.632
Nr of predictions	5

2. Individual counts for MXScarna(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	36	2	17	17	28
4A1C_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	11	2	8	1	24
4AOB_A	SAM links to Rfam database...	0.62	0.55	0.72	23	4339	10	0	9	1	19
4ENB_A	crcB links to Rfam database...	0.26	0.11	0.67	2	1272	1	0	1	0	17
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12

Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	64
Total TN	25782
Total FP	53
Total FP CONTRA	11
Total FP INCONS	36
Total FP COMP	6
Total FN	103

Total Scores
MCC	0.467
Average MCC ± 95% Confidence Intervals	0.514 ± 0.309
Sensitivity	0.383
Positive Predictive Value	0.577
Nr of predictions	5

2. Individual counts for RNASLOpt [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.